PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

DUD

DEOXYURIDINE-5'-DIPHOSPHATE

Description

Synonyms

DEOXYURIDINE-5'-DIPHOSPHATE

Formula

C9 H14 N2 O11 P2

Standard InChI

InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19...Show more

Standard InChI Key

QHWZTVCCBMIIKE-SHYZEUOFSA-N

SMILES

C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(O)OP(=O)(O)...Show more

Source OpenEye

First observed in

1duc

Overall view, and highlighted
scaffolds and fragments
This image gallery displays several views of the ligand structure:
Basic Structural Representation: Shows the overall structure of the ligand.
Detailed Structural Representation: Highlights individual atoms within the ligand.
Murcko Scaffold: Presents the scaffold of the ligand highlighted in yellow.
Highlighted Fragments: Displays various ligand fragments, highlighted in yellow.

Displayed: 1 / 7

Atom labelled DUD

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

388.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

152.9 Å ²

Heavy atoms

Number of non-hydrogen atoms

Heteroatoms

Number of non-oxygen and non-carbon atoms

Carbon SP3 value

Fraction of C atoms that are SP3 hybridized

0.6

Wildman-Crippen molar refractivity

Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability

75.0

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

0.2

Conformational properties

Rotatable bonds

Number of single bonds, not part of a ring bound to a nonterminal heavy atom

Ring properties

Aromatic rings

Number of aromatic rings

Rings

Number of rings

Aliphatic rings

Number of aliphatic rings

Heterocycles

Number or rings with at least two different elements

Saturated rings

Number of saturated rings

Aromatic heterocycles

Number of aromatic heterocyles

Saturated heterocycles

Number of saturated heterocyles

Aliphatic heterocycles

Number of aliphatic heterocycles

Spiro atoms

Atoms shared between rings that share exactly one atom

Bridgehead atoms

Number of atoms shared between rings that share at least two bonds

Surface properties

Topological surface area

197.6

Functional group properties

Hydrogen bond donors

Number of hydrogen bond donors

Hydrogen bond acceptors

Number of hydrogen bond acceptors

Amide bonds

Number of amide bonds

Stereochemical properties

Stereocenters

Number of atoms with four attachments different from each other

Bound structures

Found as a bound ligand in 11 distinct proteins and 16 PDB Structures. Group data by:

Proteins

Structures

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

dUTP diphosphatase

Q5I3E5

Paramecium bursaria Chlorella virus IL3A (PBCV-IL3A)

3.6.1.23

Unannotated

Nucleoside diphosphate kinase

Q5UQL3

Acanthamoeba polyphaga mimivirus (APMV)

2.7.4.6

Unannotated

Deoxyuridine 5'-triphosphate nucleotidohydrolase

P06968

Escherichia coli (strain K12)

3.6.1.23

Unannotated

Putative glycosyl transferase

Q9RN61

Streptomyces nogalater

Unannotated

SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS

O34919

Bacillus subtilis (strain 168)

3.6.1.23

Unannotated

Deoxyuridine 5'-triphosphate nucleotidohydrolase

P17374

Vaccinia virus (strain Western Reserve) (VACV)

3.6.1.23

Unannotated

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

P33316

Homo sapiens (Human)

3.6.1.23

Unannotated

Pol polyprotein

P11204

Equine infectious anemia virus (isolate 1369) (EIAV)

3.1.-.-, 2.7.7.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.4.23.-

Unannotated

Putative deoxyuridine triphosphatase

O15923

Trypanosoma cruzi

3.6.1.23

Unannotated

dUTP diphosphatase

F9VNI5

Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

3.6.1.23

Unannotated

Page Size:

1 to 10 of 11

Page 1 of 2

Protein name

SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS

PDB-KB Proteins

O34919

EC number

3.6.1.23

Ligand annotation

Unannotated

Total structures

Protein name

Nucleoside diphosphate kinase

PDB-KB Proteins

Q5UQL3

EC number

2.7.4.6

Ligand annotation

Unannotated

Total structures

Protein name

Deoxyuridine 5'-triphosphate nucleotidohydrolase

PDB-KB Proteins

P17374

EC number

3.6.1.23

Ligand annotation

Unannotated

Total structures

Protein name

dUTP diphosphatase

PDB-KB Proteins

Q5I3E5

EC number

3.6.1.23

Ligand annotation

Unannotated

Total structures

Protein name

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

PDB-KB Proteins

P33316

EC number

3.6.1.23

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 11

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of DUD from 47 ligand instances in 11 distinct proteins and 16 PDB Structures. The protein-ligand interactions are computed using PDBe Arpeggio

Documentation

Ligand atoms

Sort by:

Amino acid properties

Interactions

Ligand interactions

Percentage of interactions by ligand atom compared to the total interactions of the ligand

Amino acid interactions

Percentage of interactions between ligand atom-amino acid pair compared to the total interactions of the amino acid

Icons:

Positively charged

Negatively charged

Polar

Hydrophobic

Aromatic

Aromatic (Trp)

Glycine

Cysteine

Proline

Atom-wise interactions of DUD molecule
Percentage of interactions by ligand atom compared to the total interactions of the ligand

For full interaction statistics, including the heatmap showing ligand atom interaction frequency with different amino acids, please view on a larger screen